import ast
import collections
import copy
import inspect
import math
import os
import re
import sys
import uuid
from builtins import chr, map, str
from operator import attrgetter
from typing import Dict, List, Optional, Tuple
import astropy.units as u
import numba as nb
import numpy as np
import six
from yaml.reader import ReaderError
from astromodels.core.memoization import memoize
from astromodels.core.my_yaml import my_yaml
from astromodels.core.parameter import Parameter
from astromodels.core.parameter_transformation import get_transformation
from astromodels.core.property import FunctionProperty
from astromodels.core.tree import Node
from astromodels.utils.logging import setup_logger
from astromodels.utils.pretty_list import dict_to_list
from astromodels.utils.table import dict_to_table
log = setup_logger(__name__)
__author__ = 'giacomov'
try:
from IPython.display import HTML, display
except:
has_ipython = False
else:
has_ipython = True
[docs]class WarningNoTests(ImportWarning):
pass
[docs]class FunctionDefinitionError(Exception):
pass
[docs]class FunctionInstanceError(Exception):
pass
[docs]class DesignViolation(Exception):
pass
[docs]class ModelAssertionViolation(Exception):
pass
[docs]class WrongDimensionality(Exception):
pass
[docs]class TestSpecificationError(Exception):
pass
[docs]class TestFailed(Exception):
pass
[docs]class DocstringIsNotRaw(ValueError):
pass
[docs]class UnknownFunction(ValueError):
pass
[docs]class UnknownParameter(ValueError):
pass
# Value to indicate that no latex formula has been given
NO_LATEX_FORMULA = '(no latex formula available)'
# A function to find the calling sequence of a function, compatible
# with both python2 and 3
def _py2to3_getargspec(function):
if sys.version_info[0] < 3:
argspec = inspect.getargspec(function)
else: # PY3
argspec = inspect.getfullargspec(function)
return argspec
# This dictionary will contain the known function by name, so that the model_parser can instance
# them by looking into this dictionary. It will be filled by the FunctionMeta meta-class.
_known_functions = {}
# The following is a metaclass for all the functions
[docs]class Function(Node):
"""
Generic Function class. Will be subclassed in Function1D, Function2D and Function3D.
"""
def __init__(self, name: Optional[str]=None, function_definition: Optional[str]=None, parameters: Optional[Dict[str, Parameter]]=None, properties: Optional[Dict[str, FunctionProperty]] = None):
# I use default values only to avoid warnings from pycharm and other software about the
# calling sequence of this contructor. We actually need to enforce its proper use,
# with this assert
if (name is None) or (function_definition is None) or (parameters is None):
log.error("improper call")
raise AssertionError()
# Set up the node
super(Function, self).__init__(name)
# Store name, number of dimensions and the latex formula
# Store also the function definition
if not 'description' in function_definition:
log.error("Function definition must contain a description")
raise AssertionError()
if 'latex' not in function_definition:
function_definition['latex'] = '$n.a.$'
self._function_definition = function_definition
# Add the parameters as children. Since the name of the key in the dictionary might
# be different than the actual name of the parameter, use the .add_child method instead
# of the add_children method
self._parameters: Dict[str, Parameter] = collections.OrderedDict()
for child_name, child in list(parameters.items()):
self._parameters[child_name] = child
# Add the parameter as a child of the function
self._add_child(child)
# Now add the properties if there are any
if properties is not None:
self._properties: Optional[Dict[str, FunctionProperty]] = collections.OrderedDict()
for child_name, child in properties.items():
self._properties[child_name] = child
# Add the parameter as a child of the function
self._add_child(child)
else:
self._properties = None
# Now generate a unique identifier (UUID) in a thread safe, multi-processing safe
# way. This is used for example in the CompositeFunction class to keep track of the different
# instances of the same function
self._uuid = "{" + str(self._generate_uuid()) + "}"
# Normal functions are able to change units, while some specific ones (such as the one from XSpec) are not.
# In this second case, this variable will contain a tuple (x_unit, y_unit), but by default it should be
# None
self._fixed_units = None
self._is_prior = False
# stores any extrernally linked functions
self._external_functions: Dict[str, "Function"] = collections.OrderedDict()
@property
def n_dim(self) -> int:
"""
:return: number of dimensions for this function (1, 2 or 3)
"""
return type(self)._n_dim
@property
def free_parameters(self) -> Dict[str, Parameter]:
"""
Returns a dictionary of free parameters for this function
:return: dictionary of free parameters
"""
free_parameters = collections.OrderedDict(
[(k, v) for k, v in list(self.parameters.items()) if v.free])
return free_parameters
@property
def has_free_parameters(self) -> bool:
"""
Returns True or False depending on if any parameters are free
"""
for p in self.parameters.values():
if p.free:
return True
return False
def _get_parameters(self) -> Tuple[Parameter]:
"""
return a tuple of parameters
similar to get_children but for functions
"""
return tuple(self._parameters.values())
@property
def properties(self) -> Optional[Dict[str, FunctionProperty]]:
"""
return the properties of the function
:returns:
"""
return self._properties
@property
def has_properties(self) -> bool:
return self._properties is not None
[docs] def link_external_function(self, function: "Function", internal_name: str ):
"""
link and external function to this function for use in its evaluate method.
the function can be from another source
the linked function can be accessed via self.external_functions[internal_name]
:param function: the function to link.
:type function: "Function"
:param internal_name: the internal name used to access this in the external_functions dict
:type internal_name: str
:returns:
"""
if not isinstance(function, Function):
log.error("external functions must be of type Function")
raise RuntimeError()
if internal_name in self._external_functions:
log.error(f"a function with internal name {internal_name} is already linked!")
raise RuntimeError()
self._external_functions[internal_name] = function
log.debug(f"{self.name} has now linked {function.name} as {internal_name}")
[docs] def unlink_external_function(self, internal_name: str):
"""
unlink an external function
:param internal_name:
:type internal_name: str
:returns:
"""
if internal_name not in self._external_functions:
log.error(f"{internal_name} is not linked.")
log.error(f"Have {','.join(list(self._external_functions.keys()))}")
raise RuntimeError()
self._external_functions.pop(internal_name)
[docs] def unlink_all_external_functions(self):
"""
unlinks all external functions from this function
:returns:
"""
names = list(self._external_functions.keys())
for n in names:
self._external_functions.pop(n)
@property
def external_functions(self):
return self._external_functions
[docs] def to_dict(self, minimal: bool=False):
data = super(Function, self).to_dict(minimal)
if not minimal:
# link the external functions
# by there internal name and
# their path
if self._external_functions:
data["external_functions"] = collections.OrderedDict()
for k,v in self._external_functions.items():
data["external_functions"][k] = v.path
return data
@staticmethod
def _generate_uuid():
"""
Generate a unique identifier for this function.
:return: the UUID
"""
return uuid.UUID(bytes=os.urandom(16), version=4)
[docs] def has_fixed_units(self) -> bool:
"""
Returns True if this function cannot change units, which is the case only for very specific functions (like
models from foreign libraries like Xspec)
:return: True or False
"""
return not (self._fixed_units is None)
@property
def is_prior(self) -> bool:
"""
Returns False by default and must be overrided in the prior functions.
:return: True or False
"""
return self._is_prior
@property
def fixed_units(self):
"""
Returns the fixed units if has_fixed_units is True (see has_fixed_units)
:return: None, or a tuple (x_unit, y_unit)
"""
return self._fixed_units
@property
def description(self) -> str:
"""
Returns a description for this function
"""
return self._function_definition['description']
# Add a property returning the parameters dictionary
@property
def parameters(self) -> Dict[str, Parameter]:
"""
Returns a dictionary of parameters
"""
return self._parameters
@property
def latex(self):
"""
Returns the LaTEX formula for this function
"""
return self._function_definition['latex']
# Define now all the operators which allow to combine functions. Each operator will return a new
# instance of a CompositeFunction, which can then be used as a function on its own
[docs] def of(self, another_function):
"""
Compose this function with another as in this_function(another_function(x))
:param another_function: another function to compose with the current one
:return: a composite function instance
"""
return CompositeFunction('of', self, another_function)
def __neg__(self):
return CompositeFunction('*-', self)
def __abs__(self):
return CompositeFunction('abs', self)
def __pow__(self, other_instance):
return CompositeFunction('**', self, other_instance)
def __rpow__(self, other_instance):
return CompositeFunction('**', other_instance, self)
def __add__(self, other_instance):
return CompositeFunction('+', self, other_instance)
__radd__ = __add__
def __sub__(self, other_instance):
return CompositeFunction('-', self, other_instance)
def __rsub__(self, other_instance):
return CompositeFunction('-', other_instance, self)
def __mul__(self, other_instance):
c = CompositeFunction('*', self, other_instance)
# If the other instance is a function (and not a number), flag it so its units will be made dimensionless
# in the set_units method of the composite function
if isinstance(other_instance, Function):
if self.has_fixed_units():
# This is likely a XSpec model. The multiplication of two models with units will give the wrong
# units to the results. So, depending on the type of the first and second model, we need to adjust
# their units so that the result will keep the right units.
if not u.Unit(self.fixed_units[1]) == u.dimensionless_unscaled:
# This function has fixed unit and is not dimensionless (likely an additive XSpec model).
# We need to make the other function dimensionless so that the multiplication of them will keep
# the right units
other_instance._make_dimensionless = True
log.debug(f"{other_instance} is not dimensionless")
else:
# This function has fixed unit, but it is dimensionless (likely a multiplicative XSpec model)
# The other function should keep its units, so we flag self instead
self._make_dimensionless = True
log.debug("{self} is now dimensionless")
# However, if also the other function has fixed dimension and it is dimensionless
# (likely another XSpec multiplicative model) we need to flag that as well
if other_instance.has_fixed_units() and \
(u.Unit(other_instance.fixed_units[1]) == u.dimensionless_unscaled):
other_instance._make_dimensionless = True
# Now we need to flag the composite function as fixed units and dimensionless
c._fixed_units = other_instance.fixed_units
log.debug(f"{c.name} is completely dimensionless")
else:
# We need to make the other instance dimensionless so that this function (which is not dimensionless)
# multiplied by the other function (which we will make dimensionless) will give the right units as
# the results
other_instance._make_dimensionless = True
log.debug(f"{other_instance} is not dimensionless")
return c
__rmul__ = __mul__
def __div__(self, other_instance):
c = CompositeFunction('/', self, other_instance)
# If the other instance is a function (and not a number), flag it so its units will be made dimensionless
# in the set_units method of the composite function
if isinstance(other_instance, Function):
if self.has_fixed_units():
# This is likely a XSpec model. Division is not supported.
raise NotImplementedError(
"Division for XSpec models is not supported")
else:
# We need to make the other instance dimensionless
other_instance._make_dimensionless = True
return c
def __rdiv__(self, other_instance):
return CompositeFunction('/', other_instance, self)
__truediv__ = __div__
__rtruediv__ = __rdiv__
def _repr__base(self, rich_output):
repr_dict = collections.OrderedDict()
repr_dict['description'] = self._function_definition['description']
if 'latex' in self._function_definition:
repr_dict['formula'] = self._function_definition['latex']
# Add the description of each parameter and their current value
repr_dict['parameters'] = collections.OrderedDict()
for parameter in self._get_children():
repr_dict['parameters'][parameter.name] = parameter.to_dict()
return dict_to_list(repr_dict, rich_output)
@property
def uuid(self):
"""
Returns the ID of the current function. The ID is used by the CompositeFunction class to keep track of the
unique instances of each function. It should not be used by the user for any specific purpose.
:return: (none)
"""
return self._uuid
def __eq__(self, o):
return self._uuid == o.uuid
[docs] def duplicate(self):
"""
Create a copy of the current function with all the parameters equal to the current value
:return: a new copy of the function
"""
# Create a copy
function_copy = copy.deepcopy(self)
return function_copy
[docs] def get_boundaries(self): # pragma: no cover
"""
Returns the boundaries of this function. By default there is no boundary, but subclasses can
override this.
:return: a tuple of tuples containing the boundaries for each coordinate (ra_min, ra_max), (dec_min, dec_max)
"""
raise NotImplementedError("You have to implement this")
def __call__(self, *args): # pragma: no cover
raise NotImplementedError("You have to implement this")
[docs] def fast_call(self, *args): # pragma: no cover
raise NotImplementedError("You have to implement this")
[docs] def evaluate_at(self, *args, **parameter_specification): # pragma: no cover
"""
Evaluate the function at the given x(,y,z) for the provided parameters, explicitly provided as part of the
parameter_specification keywords.
:param *args:
:param **parameter_specification:
:return:
"""
# Set the parameters to the provided values
for parameter in parameter_specification:
self._get_child(
parameter).value = parameter_specification[parameter]
return self(*args)
[docs] def get_total_spatial_integral(self, z):
"""
Returns the total integral (for 2D functions) or the integral over the spatial components (for 3D functions).
needs to be implemented in subclasses.
:return: an array of values of the integral (same dimension as z).
"""
raise NotImplementedError("You have to implement this")
[docs]class Function1D(Function):
def __init__(self,name: Optional[str] = None, function_definition: Optional[str]=None, parameters: Optional[Dict[str, Parameter]] =None, properties: Optional[Dict[str, FunctionProperty]] = None):
Function.__init__(self, name, function_definition, parameters, properties)
self._x_unit = None
self._y_unit = None
[docs] def evaluate(self, x, *args, **kwargs): # pragma: no cover
raise NotImplementedError("You have to re-implement this")
[docs] def set_units(self, in_x_unit, in_y_unit):
# Transform None in input to '', so that u.Unit() will generate a dimensionless unit
in_x_unit = in_x_unit if in_x_unit is not None else ''
in_y_unit = in_y_unit if in_y_unit is not None else ''
# Get a Unit instance from the inputs
try:
in_x_unit = u.Unit(in_x_unit)
in_y_unit = u.Unit(in_y_unit)
except:
raise TypeError("Could not get a Unit instance from provided units %s when setting units "
"for function %s" % ((in_x_unit, in_y_unit), self.name))
# Now call the underlying method to set units, which is defined by each function
new_units = self._set_units(in_x_unit, in_y_unit)
# Store the units.
# NOTE: the previous call to _set_units might return new units in special cases
# (for example Xspec functions). So it is critical that we store them in the class' attributes
# after the call to _set_units
if new_units is not None:
new_x_unit, new_y_unit = new_units
self._x_unit = new_x_unit
self._y_unit = new_y_unit
else:
self._x_unit = in_x_unit
self._y_unit = in_y_unit
def _set_units(self, x_unit, y_unit): # pragma: no cover
# This will be overridden by derived classes
raise NotImplementedError(
"You have to implement the method _set_units for function %s" % self.name)
@property
def x_unit(self):
"""
The unit of the independent variable
:return: a astropy.Unit instance
"""
return self._x_unit
@property
def y_unit(self) -> u.Unit:
"""
The unit of the dependent variable
:return: a astropy.Unit instance
"""
return self._y_unit
def __call__(self, x):
# This method's code violates explicitly duck typing. The reason is that astropy.units introduce a very
# significant overload on any computation. For this reason we treat differently the case with units from
# the case without units, so that the latter case remains fast. Also, transforming an input
# which is not an array into an array introduce a significant overload (10 microseconds or so), so we perform
# this transformation only when strictly required
# NOTE: for a single quantity such as q = (1.0 * u.keV), isinstance(q, np.ndarray) returns True
if isinstance(x, np.ndarray):
# We have an array as input (or a single quantity)
if not isinstance(x, u.Quantity):
# This is a normal array, let's use the fast call (without units)
return self.fast_call(x)
else:
# This is an array with units or a single quantity, let's use the slow call which preserves units
if self.y_unit is None:
log.error("In order to use units you need to use the function as a spectrum or " \
"as something else, or you need to explicitly set the units.")
raise AssertionError()
# we want to make sure this is an array
new_input = np.atleast_1d(x)
results = self._call_with_units(new_input)
# Now convert to the expected y unit and return a astropy.Quantity by multiplying by the right unit
return np.squeeze(results.to(self.y_unit).value) * self.y_unit
else:
# This is either a single number or a list
# Transform the input to an array of floats. If x is a single number, this will be an array of size 1
new_input = np.array(x, dtype=float, ndmin=1, copy=False)
# Compute the function
result = self.fast_call(new_input)
# Now remove all dimensions of size 1. For example, an array of shape (1,) will become a single number,
# so that if the input was a single number, also the output will be a single number
sq = np.squeeze(result)
# if this is still a list after all this work this its
# shape will be
if sq.shape:
return sq
else:
# this is a single number and we assume it is a float
return np.float64(sq)
def _call_with_units(self, x):
# Gather the current parameters' values with units
values = list(map(attrgetter("as_quantity"), self._get_parameters()))
try:
results = self.evaluate(
x.to(self.x_unit, equivalencies=u.spectral()), *values)
except u.UnitsError: # pragma: no cover
# see if this is a dimensionless function
if self.has_fixed_units():
try:
results = self.evaluate(x.to(self.x_unit), *values)
except u.UnitsError:
log.error("Looks like you didn't provide all the units, or you provided the wrong ones, when "
"calling function %s" % self.name)
raise u.UnitsError()
else:
log.error("Looks like you didn't provide all the units, or you provided the wrong ones, when "
"calling function %s" % self.name)
raise u.UnitsError()
else:
return results
[docs] @memoize
def fast_call(self, x) -> np.ndarray:
# Gather the current parameters' values without units, which means that the whole computation
# will be without units, with a big speed gain (~10x)
# NOTE: it is important to use value, and not _value, to support linking
#values = list(map(attrgetter("value"), self._get_children()))
values = list(map(attrgetter("value"), self._get_parameters()))
return self.evaluate(x, * values)
[docs] def get_boundaries(self):
"""
Returns the boundaries of this function. By default there is no boundary, but subclasses can
override this.
:return: a tuple of tuples containing the boundaries for each coordinate (ra_min, ra_max), (dec_min, dec_max)
"""
log.error("Cannot call get_boundaries() on a 1d function")
raise DesignViolation()
[docs] def local_spectral_index(self, x, epsilon=1e-5):
"""
compute the local spectral index of the model at
a given set of energies
:param x:
:type energy:
:param epsilon:
:type epsilon:
:returns:
"""
a = self(x)
b = self(x * (1 + epsilon))
return _local_deriv(a, b, epsilon)
@nb.njit
def _local_deriv(a, b, epsilon):
return np.log(b / a) / math.log(1. + epsilon)
[docs]class Function2D(Function):
def __init__(self, name: Optional[str] = None, function_definition: Optional[str]=None, parameters: Optional[Dict[str, Parameter]] =None, properties: Optional[Dict[str, FunctionProperty]] = None ):
Function.__init__(self, name, function_definition, parameters, properties)
self._x_unit = None
self._y_unit = None
self._z_unit = None
[docs] def evaluate(self, x, y, *args): # pragma: no cover
raise NotImplementedError("You have to re-implement this")
[docs] def set_units(self, in_x_unit, in_y_unit, in_z_unit):
# Change None to '' for the inputs so that the following u.Unit construction will generate a dimensionless
# unit (it would fail with None)
in_x_unit = in_x_unit if in_x_unit is not None else ''
in_y_unit = in_y_unit if in_y_unit is not None else ''
in_z_unit = in_z_unit if in_z_unit is not None else ''
try:
in_x_unit = u.Unit(in_x_unit)
in_y_unit = u.Unit(in_y_unit)
in_z_unit = u.Unit(in_z_unit)
except:
raise TypeError("Could not get a Unit instance from provided units when setting units "
"for function %s" % self.name)
# Store the Unit instances
self._x_unit = in_x_unit
self._y_unit = in_y_unit
self._z_unit = in_z_unit
# Now call the underlying method to set units, which is defined by each function
self._set_units(self._x_unit, self._y_unit, self._z_unit)
def _set_units(self, x_unit, y_unit, z_unit): # pragma: no cover
# This will be overridden by derived classes
raise NotImplementedError(
"You have to implement the method _set_units for function %s" % self.name)
@property
def x_unit(self):
return self._x_unit
@property
def y_unit(self):
return self._y_unit
@property
def z_unit(self):
return self._z_unit
def __call__(self, x, y, *args, **kwargs):
# This method's code violates explicitly duck typing. The reason is that astropy.units introduce a very
# significant overload on any computation. For this reason we treat differently the case with units from
# the case without units, so that the latter case remains fast. Also, transforming an input
# which is not an array into an array introduce a significant overload (10 microseconds or so), so we perform
# this transformation only when strictly required
assert type(x) == type(y), "You have to use the same type for x and y"
if isinstance(x, np.ndarray):
# We have an array or a quantity as input
if not isinstance(x, u.Quantity):
# This is a normal array, let's use the fast call (without units)
return self._call_without_units(x, y)
else:
# This is an array with units or a single quantity, let's use the slow call which preserves units
results = self._call_with_units(x, y)
# Now convert to the expected z unit and remove useless dimensions
return np.squeeze(results.to(self.z_unit).value) * self.z_unit
else:
# This is either a single number or a list
# Transform the input to an array of floats
new_x = np.array(x, dtype=float, ndmin=1, copy=False)
new_y = np.array(y, dtype=float, ndmin=1, copy=False)
# Compute the function
result = self._call_without_units(new_x, new_y)
# Now remove all dimensions of size 1. For example, an array of shape (1,) will become a single number.
return np.squeeze(result)
def _call_with_units(self, x, y):
# Gather the current parameters' values with units
values = list(map(attrgetter("as_quantity"), self._get_parameters()))
try:
results = self.evaluate(x, y, *values)
except u.UnitsError: # pragma: no cover
raise u.UnitsError("Looks like you didn't provide all the units, or you provided the wrong ones, when "
"calling function %s" % self.name)
else:
return results
@memoize
def _call_without_units(self, x, y):
# Gather the current parameters' values without units, which means that the whole computation
# will be without units, with a big speed gain (~10x)
values = list(map(attrgetter("value"), self._get_parameters()))
return self.evaluate(x, y, *values)
[docs]class Function3D(Function):
def __init__(self, name: Optional[str] = None, function_definition: Optional[str]=None, parameters: Optional[Dict[str, Parameter]] =None, properties: Optional[Dict[str, FunctionProperty]] = None):
Function.__init__(self, name, function_definition, parameters, properties)
self._x_unit = None
self._y_unit = None
self._z_unit = None
self._w_unit = None
[docs] def evaluate(self, x, y, z, *args, **kwargs): # pragma: no cover
raise NotImplementedError("You have to re-implement this")
[docs] def set_units(self, in_x_unit, in_y_unit, in_z_unit, in_w_unit):
# Change None to '' for the inputs so that the following u.Unit construction will generate a dimensionless
# unit (it would fail with None)
in_x_unit = in_x_unit if in_x_unit is not None else ''
in_y_unit = in_y_unit if in_y_unit is not None else ''
in_z_unit = in_z_unit if in_z_unit is not None else ''
in_w_unit = in_w_unit if in_w_unit is not None else ''
# Get instances of Unit
try:
in_x_unit = u.Unit(in_x_unit)
in_y_unit = u.Unit(in_y_unit)
in_z_unit = u.Unit(in_z_unit)
in_w_unit = u.Unit(in_w_unit)
except:
raise TypeError("Could not get a Unit instance from provided units when setting units "
"for function %s" % self.name)
# Store the Unit instances
self._x_unit = in_x_unit
self._y_unit = in_y_unit
self._z_unit = in_z_unit
self._w_unit = in_w_unit
# Now call the underlying method to set units, which is defined by each function
self._set_units(self._x_unit, self._y_unit, self._z_unit, self._w_unit)
def _set_units(self, x_unit, y_unit, z_unit, w_unit): # pragma: no cover
# This will be overridden by derived classes
raise NotImplementedError(
"You have to implement the method _set_units for function %s" % self.name)
@property
def x_unit(self):
return self._x_unit
@property
def y_unit(self):
return self._y_unit
@property
def z_unit(self):
return self._z_unit
@property
def w_unit(self):
return self._w_unit
def __call__(self, x, y, z):
# This method's code violates explicitly duck typing. The reason is that astropy.units introduce a very
# significant overload on any computation. For this reason we treat differently the case with units from
# the case without units, so that the latter case remains fast. Also, transforming an input
# which is not an array into an array introduce a significant overload (10 microseconds or so), so we perform
# this transformation only when strictly required
assert type(x) == type(y) and type(y) == type(
z), "You have to use the same type for x, y and z"
if isinstance(x, np.ndarray):
# We have an array as input
if not isinstance(x, u.Quantity):
# This is a normal array, let's use the fast call (without units)
return self._call_without_units(x, y, z)
else:
# This is an array with units or a single quantity, let's use the slow call which preserves units
results = self._call_with_units(x, y, z)
# Now convert to the expected w unit and remove useless dimensions
return np.squeeze(results.to(self.w_unit).value) * self.w_unit
else:
# This is either a single number or a list
# Transform the input to an array of floats
new_x = np.array(x, dtype=float, ndmin=1, copy=False)
new_y = np.array(y, dtype=float, ndmin=1, copy=False)
new_z = np.array(z, dtype=float, ndmin=1, copy=False)
# Compute the function
result = self._call_without_units(new_x, new_y, new_z)
# Now remove all dimensions of size 1. For example, an array of shape (1,) will become a single number.
return np.squeeze(result)
def _call_with_units(self, x, y, z):
# Gather the current parameters' values with units
values = list(map(attrgetter("as_quantity"), self._get_parameters()))
try:
results = self.evaluate(x, y, z, *values)
except u.UnitsError: # pragma: no cover
raise u.UnitsError("Looks like you didn't provide all the units, or you provided the wrong ones, when "
"calling function %s" % self.name)
else:
return results
@memoize
def _call_without_units(self, x, y, z):
# Gather the current parameters' values without units, which means that the whole computation
# will be without units, with a big speed gain (~10x)
values = list(map(attrgetter("value"), self._get_parameters()))
return self.evaluate(x, y, z, *values)
##########################
# Composite function stuff
##########################
# Codes to indicate to Composite Function the operation between two functions
_operations = {'+': np.add,
'-': np.subtract,
'*-': np.negative,
'*': np.multiply,
'/': np.divide,
'**': np.power,
'abs': np.abs,
'of': 'compose'}
# These methods need to be here to overcome the limitation of pickle with methods of classes
def _cf_evaluate_func_func(np_operator, f1, f2, *args):
# Evaluate for when both elements are functions
return np_operator(f1(*args), f2(*args))
def _cf_evaluate_func_number(np_operator, f1, f2, *args):
# Evaluate for when element 1 is a function and element 2 is a number
return np_operator(f1(*args), f2)
def _cf_evaluate_number_func(np_operator, f1, f2, *args):
# Evaluate for when element 2 is a function and element 1 is a number
return np_operator(f1, f2(*args))
def _cf_evaluate_func_of_func(np_operator, f1, f2, *args):
value = f2(*args)
return f1(value, *(args[1:]))
[docs]class CompositeFunction(Function):
def __init__(self, operation, function_or_scalar_1, function_or_scalar_2=None):
if not operation in _operations:
log.error("Do not know operation %s" % operation)
raise AssertionError()
# Save this to make the class pickeable (see the __setstate__ and __getstate__ methods)
self._calling_sequence = (
operation, function_or_scalar_1, function_or_scalar_2)
self._requested_x_unit = None
self._requested_y_unit = None
self._operation = operation
# Set the new __call__ according to the type of the elements in the expression
self._decide_evaluate_type()
# Save a description, but using the unique IDs of the functions involved, to keep track
# of where they appear in the expression
self._uuid_expression = self._get_uuid_expression(
operation, function_or_scalar_1, function_or_scalar_2)
log.debug(f"UUID of composite {self._uuid_expression}")
# Makes the list of unique functions which compose this composite function.
self._functions = []
for function in [function_or_scalar_1, function_or_scalar_2]:
# Check whether this is already a composite function. If it is, add the functions contained
# in it
if isinstance(function, CompositeFunction):
for sub_function in function.functions:
if sub_function not in self._functions:
self._functions.append(sub_function)
elif isinstance(function, Function):
# This is a simple function. Add it only if it is not there already (avoid duplicate)
if function not in self._functions:
self._functions.append(function)
else:
# This is a scalar, no need to add it among the functions
pass
# Make sure all functions have the same dimension, and store it so that the property .n_dim of
# the Function class will work
self._n_dim = self._functions[0].n_dim
if self._n_dim > 1:
log.error("CompositeFunction class can only handle 1-dimensional functions at the moment.")
raise NotImplementedError()
for function in self._functions:
if function.n_dim != self._n_dim:
log.error("You cannot compose functions of different dimensionality")
raise RuntimeError()
# Now assign a unique name to all the functions, to make clear which is which in the definition
# and give an easy way for the user to understand which parameter belongs to which function
self._id_to_uid = {}
expression = self._uuid_expression
for i, function in enumerate(self._functions):
self._id_to_uid[i+1] = function.uuid
expression = expression.replace(
function.uuid, "%s{%s}" % (function.name, i+1))
# Save the expression
self._expression = expression
log.debug(f"function expression: {self._expression}")
# Build the parameters dictionary assigning a new name to each parameter to account for possible
# duplicates.
parameters = collections.OrderedDict()
properties = collections.OrderedDict()
self._sub_children = collections.OrderedDict()
for i, function in enumerate(self._functions):
log.debug(f"func path before comp: {function.path}")
for parameter_name, parameter in function.parameters.items():
# New name to avoid possible duplicates
match = re.match("(.+)_[0-9]+$", parameter_name)
if match is not None:
original_name = match.groups()[0]
else:
original_name = parameter_name
new_name = f"{original_name}_{i+1}"
log.debug(f"rename {original_name} -> {new_name}")
# Store the parameter under the new name (obviously this is a reference to the
# parameter, not a copy, as always in python)
parameters[new_name] = parameter
parameter._change_name(new_name, clear_parent = False)
if function.properties is not None:
for property_name, function_property in function.properties.items():
# New name to avoid possible duplicates
match = re.match("(.+)_[0-9]+$", property_name)
if match is not None:
original_name = match.groups()[0]
else:
original_name = property_name
new_name = f"{original_name}_{i+1}"
log.debug(f"rename {original_name} -> {new_name}")
# Store the parameter under the new name (obviously this is a reference to the
# parameter, not a copy, as always in python)
properties[new_name] = function_property
function_property._change_name(new_name, clear_parent = False)
# now, some functions may have children and we want to keep track of those
self._sub_children[function.name] = collections.OrderedDict()
for child_name, child in function._children.items():
if child_name not in function.parameters:
log.debug(f"{function.name} has child {child_name}")
self._sub_children[function.name][child_name] = child.to_dict(minimal=False)
if not function.is_root:
log.warning(f"{function.name} was previously assigned to {function._root(source_only=True).name}")
log.warning(f"it has now been removed as it is a composite")
log.warning("you can create a new function and link it to the composite parameters if needed")
# if the function is attached to a source, we want to ditch the source
# because now this function is part of a composite
function = function._parent._remove_child(function.name, delete=False)
log.debug(f"func path after comp: {function.path}")
# reset properties if there were none
if not properties:
properties = None
# Now build a meaningful description
_function_definition = {
'description': self.expression, 'latex': NO_LATEX_FORMULA}
Function.__init__(self, 'composite', _function_definition, parameters, properties)
self._uuid = self._uuid_expression
[docs] def set_units(self, x_unit, y_unit, relaxed=False):
if relaxed and (x_unit is None) and (y_unit is None):
# This can happen when rebuilding a composite function during unpickling, when
# there are more than two functions composed together. We do not need to to anything in that case
pass
else:
self._requested_x_unit = x_unit
self._requested_y_unit = y_unit
# Just rely on the single functions to adjust themselves.
for function in self.functions:
if hasattr(function, '_make_dimensionless'):
function.set_units(x_unit, u.dimensionless_unscaled)
else:
function.set_units(x_unit, y_unit)
@property
def expression(self):
return self._expression
@staticmethod
def _get_uuid_expression(operation, name_1, name_2=None):
if name_2 is None:
return '(%s %s)' % (operation, name_1.uuid)
if hasattr(name_1, 'uuid'):
name_1_uuid = name_1.uuid
else:
name_1_uuid = '%s' % name_1
if hasattr(name_2, 'uuid'):
name_2_uuid = name_2.uuid
else:
name_2_uuid = '%s' % name_2
return '(%s %s %s)' % (name_1_uuid, operation, name_2_uuid)
def _decide_evaluate_type(self):
# Assign to __call__ the right evaluate according to the type of the elements in the expression
operation, self._f1, self._f2 = self._calling_sequence
np_operator = _operations[operation]
self._np_operator = np_operator
if np_operator == "compose":
assert hasattr(
self._f2, 'evaluate'), "Second member of .of cannot be a scalar"
assert self._f1.n_dim == 1 and self._f2.n_dim == 1, "Can only compose with .of functions of 1 variable"
self.evaluate = _cf_evaluate_func_of_func
else:
# Check whether the second member is a function, or a number
if hasattr(self._f1, 'evaluate'):
if hasattr(self._f2, 'evaluate'):
self.evaluate = _cf_evaluate_func_func
else:
self.evaluate = _cf_evaluate_func_number
else:
if hasattr(self._f2, 'evaluate'):
self.evaluate = _cf_evaluate_number_func
else: # pragma: no cover
# Should never get here!
raise RuntimeError("Should never get here")
@property
def functions(self):
"A list containing the function used to build this composite function"
return self._functions
[docs] def evaluate(self): # pragma: no cover
raise NotImplementedError(
"You cannot instance and use a composite function by itself. Use the factories.")
# This dumb function must be here because it is not possible to override at runtime __call__ (nor any other
# special method)
def __call__(self, x):
return self.evaluate(self._np_operator, self._f1, self._f2, x)
# For composite function, fast_call is the same as __call__ (because the call will be forwarded to the
# inner functions)
fast_call = __call__
# Override the to_dict method of the Node class to add the expression to re-build this
# composite function
[docs] def to_dict(self, minimal=False):
data = super(CompositeFunction, self).to_dict(minimal)
if not minimal:
data['expression'] = self._expression
flag = False
for function in self._functions:
if function.external_functions:
flag = True
if flag:
data['external_functions'] = collections.OrderedDict()
for i, function in enumerate(self._functions):
this_function = collections.OrderedDict()
for k,v in function.external_functions.items():
this_function[k] = v.path
data['external_functions'][i] = this_function
return data
[docs]def get_function(function_name, composite_function_expression=None):
"""
Returns the function "name", which must be among the known functions or a composite function.
:param function_name: the name of the function (use 'composite' if the function is a composite function)
:param composite_function_expression: composite function specification such as
((((powerlaw{1} + (sin{2} * 3)) + (sin{2} * 25)) - (powerlaw{1} * 16)) + (sin{2} ** 3.0))
:return: the an instance of the requested class
"""
# Check whether this is a composite function or a simple function
if composite_function_expression is not None:
# Composite function
# get the function
composite_function = _parse_function_expression(composite_function_expression)
# it is possible that the functions have sub children
return composite_function
else:
if function_name in _known_functions:
function_class = _known_functions[function_name]
deferred_properites = collections.OrderedDict()
if function_class._properties is not None:
for name, func_prop in function_class._properties.items():
# we need to specify this in hte constructor
# this will change to the saved value when the
# function is fully built
if func_prop.is_deferred:
if func_prop._allowed_values is not None:
# if there are only allowed values
# then we select the first one
deferred_properites[name] = func_prop._allowed_values[0]
else:
deferred_properites[name] = "_tmp"
# Ok, let's create the instance
instance = function_class(**deferred_properites)
return instance
else:
# Maybe this is a template
# NOTE: import here to avoid circular import
from astromodels.functions.template_model import (MissingDataFile,
TemplateModel)
try:
instance = TemplateModel(function_name)
except MissingDataFile:
log.error("Function %s is not known. Known functions are: %s" %
(function_name, ",".join(list(_known_functions.keys()))))
raise UnknownFunction()
else:
return instance
[docs]def get_function_class(function_name):
"""
Return the type for the requested function
:param function_name: the function to return
:return: the type for that function (i.e., this is a class, not an instance)
"""
if function_name in _known_functions:
return _known_functions[function_name]
else:
log.error("Function %s is not known. Known functions are: %s" %
(function_name, ",".join(list(_known_functions.keys()))))
raise UnknownFunction()
[docs]def list_functions():
# Gather all defined functions and their descriptions
functions_and_descriptions = {key: {'Description': value._function_definition['description']}
for key, value in list(_known_functions.items())}
# Order by key (i.e., by function name)
ordered = collections.OrderedDict(
sorted(functions_and_descriptions.items()))
# Format in a table
table = dict_to_table(ordered)
return table
def _parse_function_expression(function_specification):
"""
Parse a complex function expression like:
((((powerlaw{1} + (sin{2} * 3)) + (sin{2} * 25)) - (powerlaw{1} * 16)) + (sin{2} ** 3.0))
and return a composite function instance
:param function_specification:
:return: a composite function instance
"""
# NOTE FOR SECURITY
# This function has some security concerns. Security issues could arise if the user tries to read a model
# file which has been maliciously formatted to contain harmful code. In this function we close all the doors
# to a similar attack, except for those attacks which assume that the user has full access to a python environment.
# Indeed, if that is the case, then the user can already do harm to the system, and so there is no point in
# safeguard that from here. For example, the user could format a subclass of the Function class which perform
# malicious operations in the constructor, add that to the dictionary of known functions, and then interpret
# it with this code. However, if the user can instance malicious classes, then why would he use astromodels to
# carry out the attack? Instead, what we explicitly check is the content of the function_specification string,
# so that it cannot by itself do any harm (by for example containing instructions such as os.remove).
# This can be a arbitrarily complex specification, like
# ((((powerlaw{1} + (sin{2} * 3)) + (sin{2} * 25)) - (powerlaw{1} * 16)) + (sin{2} ** 3.0))
# Use regular expressions to extract the set of functions like function_name{number},
# then build the set of unique functions by using the constructor set()
unique_functions = set(re.findall(
r'\b([a-zA-Z0-9_]+)\{([0-9]?[0-9]?[0-9]?)\}', function_specification))
# NB: unique functions is a set like:
# {('powerlaw', '1'), ('sin', '2')}
# Create instances of the unique functions
instances = {}
# Loop over the unique functions and create instances
for (unique_function, number) in unique_functions:
complete_function_specification = "%s{%s}" % (unique_function, number)
# As first safety measure, check that the unique function is in the dictionary of _known_functions.
# This could still be easily hacked, so it won't be the only check
if unique_function in _known_functions:
# Get the function class and check that it is indeed a proper Function class
function_class = _known_functions[unique_function]
if issubclass(function_class, Function):
# let's see if there are any deferred
# properties
deferred_properites = collections.OrderedDict()
if function_class._properties is not None:
for name, func_prop in function_class._properties.items():
# we need to specify this in hte constructor
# this will change to the saved value when the
# function is fully built
if func_prop.is_deferred:
if func_prop._allowed_values is not None:
# if there are only allowed values
# then we select the first one
deferred_properites[name] = func_prop._allowed_values[0]
else:
deferred_properites[name] = "_tmp"
# Ok, let's create the instance
instance = function_class(**deferred_properites)
# Append the instance to the list
instances[complete_function_specification] = instance
else:
log.error("The function specification %s does not contain a proper function"
% unique_function)
raise FunctionDefinitionError()
else:
# It might be a template
# This import is here to avoid circular dependency between this module and TemplateModel.py
import astromodels.functions.template_model
try:
instance = astromodels.functions.template_model.TemplateModel(
unique_function)
except astromodels.functions.template_model.MissingDataFile:
# It's not a template
raise UnknownFunction("Function %s in expression %s is unknown. If this is a template model, you are "
"probably missing the data file" % (unique_function, function_specification))
else:
# It's a template
instances[complete_function_specification] = instance
# Check that we have found at least one instance.
if len(instances) == 0:
log.error("No known function in function specification")
raise DesignViolation()
# The following presents a slight security problem if the model file that has been parsed comes from an untrusted
# source. Indeed, the use of eval could make possible to execute things like os.remove.
# In order to avoid this, first we substitute the function instances with numbers and remove the operators like
# +,-,/ and so on. Then we try to execute the string with ast.literal_eval, which according to its documentation:
# Safely evaluate an expression node or a Unicode or Latin-1 encoded string containing a Python literal or
# container display. The string or node provided may only consist of the following Python literal structures:
# strings, numbers, tuples, lists, dicts, booleans, and None.This can be used for safely evaluating strings
# containing Python values from untrusted sources without the need to parse the values oneself.
# It is not capable of evaluating arbitrarily complex expressions, for example involving operators or indexing.
# If literal_eval cannot parse the string, it means that it contains unsafe input.
# Create a copy of the function_specification
string_for_literal_eval = function_specification
# Remove from the function_specification all the known operators and function_expressions, and substitute them
# with a 0 and a space
# Let's start from the function expression
for function_expression in list(instances.keys()):
string_for_literal_eval = string_for_literal_eval.replace(
function_expression, '0 ')
# Now remove all the known operators
for operator in list(_operations.keys()):
string_for_literal_eval = string_for_literal_eval.replace(
operator, '0 ')
# The string at this point should contains only numbers and parenthesis separated by one or more spaces
if re.match('''([a-zA-Z]+)''', string_for_literal_eval):
log.error("Extraneous input in function specification")
raise DesignViolation()
# By using split() we separate all the numbers and parenthesis in a list, then we join them
# with a comma, to end up with a comma-separated list of parenthesis and numbers like:
# ((((0,0,(0,0,3)),0,(0,0,25)),0,(0,0,16)),0,(0,0,0,3.0))
# This string can be parsed by literal_eval as a tuple containing other tuples, which is fine.
# If the user has inserted some malicious content, like os.remove or more weird stuff like code objects,
# the parsing will fail
string_for_literal_eval = ",".join(string_for_literal_eval.split())
# At this point the string should be just a comma separated list of numbers
# Now try to execute the string
try:
ast.literal_eval(string_for_literal_eval)
except (ValueError, SyntaxError):
log.error("The given expression is not a valid function expression")
raise DesignViolation()
else:
# The expression is safe, let's eval it
# First substitute the reference to the functions (like 'powerlaw{1}') with a string
# corresponding to the instance dictionary
sanitized_function_specification = function_specification
for function_expression in list(instances.keys()):
sanitized_function_specification = sanitized_function_specification.replace(function_expression,
'instances["%s"]' %
function_expression)
# Now eval it. For safety measure, I remove all globals, and the only local is the 'instances' dictionary
composite_function = eval(sanitized_function_specification, {}, {
'instances': instances})
return composite_function